CARMA statistics

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CARMA specifications

Information


Unique identifier OMICS_01451
Name CARMA
Alternative name webCARMA
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Lutz Krause <>

Information


Unique identifier OMICS_01451
Name CARMA
Alternative name webCARMA
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Lutz Krause <>

Publication for CARMA

CARMA in publications

 (22)
PMCID: 4802719
PMID: 27001503
DOI: 10.1186/s12866-016-0669-8

[…] and 80 % confidence level. the rdp classifier predicted the taxonomic origin of 16s rrna up to the rank of genus. moreover, in order to rectify diversity picture other reference databases such webcarma (based on environmental gene tags i.e. egts) and non-redundant database m5nr were also used with standard parameters., rarefaction curve was generated for all reads, except unassigned reads. […]

PMCID: 4634789
PMID: 26537885
DOI: 10.1186/s12859-015-0788-5

[…] (fig. ). there was notable increase in sensitivity and precision for methods such as megan4 and metabin which are less conservative in their predictions. for more conservative methods such as carma3 and discribinate, there was little change.fig. 3, the changes in sensitivity, precision, and taxonomic distance as read length increased was then examined. this was done on the metasimhc […]

PMCID: 4620158
PMID: 26579081
DOI: 10.3389/fmicb.2015.01166

[…] kegg (kanehisa and goto, ) classification tree using seed (may 17, 2010) and kegg (dec 1, 2010) identifiers, respectively. additionally, taxonomic and functional annotation was carried out on the webcarma v1.0 online system (http://webcarma.cebitec.uni-bielefeld.de/cgi-bin/webcarma.cgi) (gerlach et al., )., for all statistical analyses, gene counts were normalized by dividing the number […]

PMCID: 4571567
PMID: 26323759
DOI: 10.1098/rstb.2014.0328

[…] contigs with similar sequence patterns. for instance, megan [] is based on homology searches, phylopythia/s/s+ [–] and clams [] compare sequence compositions, such as oligonucleotide frequencies, carma [] performs phylogenetic reconstructions for sequence classification and phymmbl [,] uses a combination of sequence composition and blast. another hybrid approach, retrieving training sets […]

PMCID: 4713107
PMID: 26823635
DOI: 10.3767/003158515X689135

[…] done at the cbs-knaw fungal biodiversity centre. the in silico pipeline for identifying suitable protein sequences for primer design is briefly described below., the approach was inspired by the carma algorithm for taxonomic identification of metagenomic sequences (). carma matches short environmental gene fragments to pfam protein families and constructs a taxonomic profile for the sample. […]


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CARMA institution(s)
Center for Biotechnology (CeBiTec), Bioinformatics Resource Facility (BRF), Bielefeld University, Bielefeld, Germany

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